The story opens on the Planet Krypton, wherein (Ayelet Zurer), has just given birth to a son. She and her husband (Russell Crowe) have birthed their son naturally and in violation of the basic laws of the planet, where babies are to be bred through genetic engineering with a planetary 'Codex' that imprints what a person's place in life is to be (leader, scientist, general, etc).
and his wife have chosen this path as their planet is on the brink of destruction. Harvesting their planet's core for resources has made it unstable and it will destroy itself. After the birth of his son, Jor-El appears before the Kryptonian Leaders, pleading with them to allow him to save the planet's Codex, and to search for a habitable world beyond Krypton. However, even with destruction imminent, the council will not abandon its ways.
The council is set upon by (Michael Shannon) and numerous followers, intending to take control of the planet. Though Jor-El does disagree with Council, he refuses to join Zod's coup. Zod orders Jor-El to be arrested, but Jor-El escapes and flees to an area nearby, wherein the planet's birthing chamber resides. Right before he leaves, he tells Lara to prepare the small spacecraft he has built to transport his son from Krypton and to find a suitable world to send him to.
Stealing the Codex from the chamber, Jor-El races back to his home where his wife Lara has found a planet to send their baby to: Earth. Though Lara is sad at the loss of their child, Jor-El claims he will live his life in a new way: free of the limitations imposed by Kryptonian society. Their son, Kal-El, will be able to choose his way in life. Lara worries about their son's ability to survive on his new planet; Jor-El assures her he will be stronger, faster, invulnerable and possess powers that will make him a super-being there because of Earth's yellow sun. Jor-El places the Codex into a device that bonds it to his son's living cells.
As they prepare to launch the pod containing their son, Zod and his followers force their way into the Els residence, demanding that Jor-El hand over the Codex. Jor-El claims it is in the pod with his son. Zod becomes enraged and attacks Jor-El, eventually stabbing him to death. During the fight, Lara engages the pod's engines and it shoots into the sky.
Angered that Jor-El and his wife have doomed the Kryptonian race with the removal of the Codex, Zod orders his followers to shoot down the pod. However, his orders are suddenly cancelled when Kryptonian security ships appear, destroying the attacking vessel and arresting Zod and his minions. In the confusion, the small craft's propulsion engine, a Phantom Drive, engages on the pod, rocketing the baby away in the blink of an eye.
Zod and his followers are banished to The Phantom Zone. In a fury, Zod lashes out, declaring the leaders will not grant him and his followers a quick death. He also swears to Lara (who is present), that he will find her son. Zod and his followers are placed in a giant craft, the Black Zero, that is sent into the Phantom Zone.
Shortly after, Krypton's core collapses as Lara passively watches the planet breaking apart. Many worlds away, the pod carrying Kal-El rockets into Earth's atmosphere, touching down somewhere in the Great Plains of the United States.
The scene then shifts to ocean waters, where we see a bearded man (Henry Cavill) working aboard a fishing vessel and having trouble concentrating on his duties.The crew are soon alerted to a distress call for help from a flaming oil rig. The bearded man quickly disappears from the ship but is on the rig moments later, rescuing the crew and getting them to board a Coast Guard chopper. He is unable to join them, as he rushes to keep a part of the rig from collapsing on the landing pad. As the chopper flies away with the rig's crew, the rig collapses down on him and he ends up floating in the water.
We soon learn that this is , as in a deep mental state, he recalls when he was younger, and manifested X-Ray vision, and super-hearing. Scared at what he was seeing and hearing, Clark runs from his classroom and locks himself in a closet. His Mother comes to the school, and manages to coax him out, helping him to focus his powers, quelling the myriad sounds he hears.
Back in the present-day, Clark has managed to return to land and steals some clothes. As he attempts to figure out where he is, he sees a school bus nearby. Clark has another flashback to when he was 13. He recalls being picked on by a boy named (Jack Foley), before the school bus they were on suddenly blows a tire, and careens off a bridge into a river. Thinking quickly, Clark escapes out the rear emergency door, and pushes the bus to shore. Clark jumps back into the water and pulls the very boy who harassed him to safety.
Though Pete's mother claims that Clark miraculously saved the occupants of the bus, Clark's father (Kevin Costner) tries to convince her otherwise. Needless to say, Clark feels even more conflicted, as his father has tried to tell him to suppress his powers, but Clark was torn by a need to help others.
When Clark demands to know what's wrong with him, Jonathan shows his son the pod he came to Earth in, along with a strange metallic item that was found with him. Jonathan claims he had a metallurgist examine it, but it is comprised of elements not found on Earth. Imprinted on the small fragment of metal is a shield-like shape containing an "S".
The scene then returns to the present day, where Clark has a job at a truck stop in Canada. As he works, he hears some military men talking quietly about some object found in the ice a ways north of the stop. When a trucker comes in and starts harassing one of the waitresses, Clark attempts to stop him, but afraid others will see his powers, stands there and takes the trucker's taunts. Without saying a word, Clark takes off his apron and leaves the stop. Later, as the trucker leaves, he is shocked to find his rig impaled on several of the large logs he was hauling.
The scene then cuts to (Amy Adams), landing at the base in Canada, where she is met by (Richard Schiff), and (Christopher Meloni). Drilling is still commencing within the ice to get to uncover the craft, but ice drilling tests have at least confirmed that the ice surrounding the object is thousands of years old.
Going out in the evening to shoot some pictures, Lois is shocked when she checks them to see a man walking on a ridge near the drilling site without cold-weather clothing. She sneaks up to where he was, and finds a tunnel bored into the ice. The tunnel is Clark's doing, as he had followed the word of the military men, and made his way to the site, using his heat vision to create the tunnel through solid ice. He then finds a strange spacecraft, and going inside, finds a panel that opens up. It contains a hole that seems to match the shape of the object his father found with him in the pod. Inserting the object the hole causes a person to suddenly appear nearby. He doesn't say a word, simply walking off. Clark attempts to catch up to this person, but he always seems to be several steps ahead of him.
Meanwhile, Lois has found her way onto the ship, but is attacked by a sentry. Her screams cause Clark to come running. After dismantling the sentry by crushing it with his bare hands, he sees that the sentry has wounded Lois in her lower abdomen. He tells her she's bleeding internally and uses his heat vision to cauterize the wound. Shortly after, military forces nearby are all amazed when the ice starts to crack and a giant ship emerges, flying off.
Lois is found the next day and shortly thereafter she writes up an article about what she experienced. However, her editor at the Daily Planet, (Laurence Fishburne), refuses to publish it. Even the Pentagon has denied her 'aliens and spaceships' story. Lois then attempts to play hard ball. Going to a contact of hers named (Chad Krowchuk), she allows him to publish her story. Though he cautions that she could get in trouble for leaking the story, she claims she wants to do this, in hopes that it will catch the attention of the person she met.
Meanwhile, Clark has piloted the spaceship to another remote location in the Arctic. It turns out the figure he was following is a hologram of his father Jor-El, who is appearing via the 'key' Clark inserted into the ship. Jor-El explains the history of the planet Krypton, Zod's attempted coup and that the ship Clark found was a sentry ship sent out many years before, when the the council of Krypton had sought to colonize other planets.
Jor-El shows Clark a dark blue and red suit bearing the shielded "S". Jor-El explains that it is the emblem of the House of El and a symbol of hope. Jor-El also explains that the Earth's sun has made Clark stronger than human beings, and has been helping him manifest powers for some time. Jor-El tells Clark that the suit will symbolize his mission: to help the people of Earth and act as their guardian. Stepping outside the ship, Clark begins to push his powers: first taking flying leaps, before eventually being able to fly at great speeds, breaking the sound barrier and flying great distances around the world.
Back in Metropolis, is furious that Lois leaked her story to the internet, and suspends her for three weeks. Lois uses this time to begin tracking down leads to her mystery man. Her sleuthing leads her to Smallville, and eventually, .
Visiting the grave of Jonathan Kent, she is surprised when her mystery man appears (albeit in nondescript clothing). Lois claims she wants to tell Clark's story, but he tells her of how he abides by his father's request to not reveal himself until the world 'was ready.'
Clark then relates how Jonathan died. After the two have an argument during a drive, which mostly concerns Clark frustration over his true ancestry and how he is forbidden to reveal his powers to anyone but his parents, they stop when a tornado forms, threatening everyone on the road nearby. Clark gets his mother and several others to safety, with Jonathan attempting to get the family dog free of their vehicle. The dog makes it out safely, but Jonathan suffers an injury to his ankle and is unable to make it to the overpass where everyone has taken shelter. Clark had wanted to help his father, but a gesture from Jonathan cautioned him to not reveal himself, leaving Jonathan to be swept away by the tornado. Hearing his story, Lois respects Clark's wish for privacy, and stops trying to pursue a story from him.
Clark returns to his mother, and happily tells her that he has found where he came from, and who his true parents are. Though Martha fears that her son will now be taken from her, Clark assures her it won't happen.
Meanwhile, the military has detected a strange ship in geosynchronous orbit around the planet. Others soon report the strange sighting, but are surprised when power is cut off to all parts of the world, and a message is broadcast from General Zod. Zod demands that the people of Earth hand over Kal-El within 24 hours or there will be consequences. A worldwide manhunt is initiated to find this "Kal-El". Glenn Woodburn is interviewed about the aliens and drops Lois' name, which soon results in numerous FBI agents being sent to take her into custody. Lois tries to flee from them, but she's quickly intercepted and turned over to the US Army.
Back in Smallville, Clark goes to a local church, and confesses to the pastor that he is the one the aliens want. Clark admits he is conflicted: he doesn't trust that Zod will leave Earth in peace, but he is also wondering if he should trust humanity. His decision is made when the Pastor tells him that sometimes one must take a leap of faith.
Clark then appears before the Army in his Kryptonian suit, willing to surrender on condition that he can meet with Lois and that she be freed. Clark is handcuffed (he allows them to, as a gesture of trust and to help them feel more secure), and he and Lois have a short conversation. She asks him about the "S" on his chest which he tells her is not an S as Earthlings know it, but a symbol of hope. When she suggests a new moniker, her voice is cut off by feedback from the audio system observers are using behind a 2-way mirror -- but Clark shows he is easily able see through it and identify the people standing behind it. Clark stands up and effortlessly breaks his handcuffs and tells the observers he'll allow them to turn him over to Zod and that he'll protect the planet from whatever danger Zod presents.
In a remote desert, a black craft appears to bring him to Zod's ship. The craft is commanded by (Antje Traue), who also demands of (Harry Lennix), that Lois also be taken with them. Though Swanwick points out that the deal was originally for only Kal-El to be handed over, Lois agrees to go with Clark. Before they reach Zod's ship, Lois is fitted with a breathing apparatus, as the atmosphere on the ship will be toxic to humans. When Faora is distracted, Clark slips Lois the key he used to restart the Arctic ship.
On board the Black Zero, Zod welcomes Clark, who a few moments later collapses to the floor of the ship, seemingly unable to breathe. Though Lois is worried for him, Zod assures her that Clark's body is simply adjusting to the Kryptonian atmosphere aboard the ship.
Clark passes out, and finds himself in a dreamlike vision of his family's farm. Zod explains to Clark that after the destruction of Krypton, the portal to the Phantom Zone where they were trapped was broken open. After modifying the portal's Phantom Drive, they were able to transport themselves all across the galaxy in the Black Zero. Visiting the various planets which colonizing ships were sent, their searches for a new planet proved unfruitful, as each of the colonists sent to these various planets were found to have perished. However, Zod and his followers took what they could from the remnants of their civilization, including a terraforming machine called a "World Engine".
When Clark activated the ship in the Arctic, it sent out a signal, which lead Zod to Earth. Zod claims that he intends to turn Earth into a New Krypton, but Clark is unwilling to go along with this plan since it will mean Earth's annihilation and the deaths of all humans.
Awakening from the vision, Zod tells Clark that with or without him, he will revive their civilization. As well, Clark's adjustments to the ship have made him no stronger than the other Kryptonians on it. Consequently, one of Zod's men, (Mackenzie Gray), is able to obtain a blood sample from Clark.
Meanwhile, Lois is thrown into a holding cell, where she comes across a panel with a small hole. Lois notes it is the same shape as the key she has. Inserting it allows the information from Jor-El to appear before her. The key causes the ship's atmosphere to alter towards more suitable conditions for Clark and Lois, and Jor-El gives Lois valuable information for stopping Zod, along with leading her to an escape pod. As she activates the pod a guard suddenly shoots at her, damaging the pod. The change in the atmosphere returns Clark's strength, allowing him to break his bonds, and Jor-El appears before him, pointing out that Lois needs to be saved because of the damage to the pod.
Clark saves Lois from the pod, but his attention is soon drawn to his mother, who is set upon by Zod and Faora. Zod goes to the Kent farm, looking for the Codex. Faora finds Clark's pod, but no sign of the Codex. When Zod threatens Martha, Clark races to save her, hitting Zod with such force that the two end up thrown into the heart of downtown Smallville. Upon recovering, Zod's face-mask malfunctions and his body begins to adapt to the Earthen environment, as he suddenly gains X-Ray vision, and his hearing begins to take in everything at once (just like Clark did when he gained these powers long ago). The effect is debilitating to Zod as his senses overload and he is forced to retreat.
Clark claims that his parents helped him hone his skills to control the sensory overload, but his assurance is thrown aside when a ship recovers the stunned Zod, and Faora and a larger Kryptonian (Nam-Ek) attempt to bring Clark down. A battle erupts between Clark and his enemies, causing huge amounts of destruction.
Word of the alien presence in Smallville has reached the Army, and Col. Hardy approaches with helicopters and planes. Hardy claims that all three of the aliens (including Clark) are hostile, and all forms of weaponry are thrown at them. Though Faora and Nam-Ek escape, Clark is able to change Hardy's mind when he saves the Colonel along with several other soldiers.
Clark returns to his mother, but also encounters Lois, who explains to him what Jor-El told her on the ship.
Back on his ship, Zod is informed what happened to the Codex. Jor-El had diffused it into Clark's cells, making him the source to create new Kryptonian life. When Zod is informed that Clark does not need to be taken alive to retrieve the Codex, he puts his plan into effect.
Zod separates the World Engine from the Black Zero. As it touches down in the South Indian Ocean, the Black Zero hovers over Metropolis. Using the Phantom Drive, Zod activates the World Engine, which creates a link with the Black Zero through the Earth's core, beginning the process of terraforming Earth into a planet more like Krypton. Dr. Emil Hamilton determines that the process is creating a stronger gravitational pull and making the planet more dense. The effect causes massive destruction, flattening cars and shaking skyscrapers apart. The force of the machine also causes objects to repeatedly rise and plummet to Earth.
As Swanwick contemplates what to do, he receives word that Clark (now being called "Superman" by some of the soldiers), has a plan. Using the information that Lois obtained, Clark reasons that if the pod that brought him to Earth is activated by the key he has it will start up the Phantom Drive inside. If the pod collides with Zod's ship which also has its drive activated, a black hole will warp the Black Zero and it's occupants back into the Phantom Zone.
Meanwhile, Zod leaves his ship, and heads for the ship Clark found in the Arctic. On board the ship is a gestation chamber with many unborn Kryptonian fetuses. The projection of Jor-El speaks to Zod, telling him to halt his operation. Zod refuses to listen to the words of a ghost. and will stop at nothing to revive Krypton and it's people. Zod's key eventually overrides Jor-El's, and the ship now responds to Zod, causing Jor-El's hologram to disappear.
Col Hardy, Dr Hamilton, and Lois board a plane to take the pod to Metropolis, while Superman flies around the world to try and stop the World Engine. However, he is assailed by a Kryptonian defense mechanism within the machine that attempts to fend him off with long tentacles.
The situation over Metropolis grows more desperate as none of the planes sent by the Air Force are able to get close to the Black Zero. Zod's ship and the World Engine have created a gravitational vacuum that keeps the transport unable to properly launch Clark's pod. Realizing there's no way he can fight off the tentacles, Clark goes deep under the World Engine and punches his way through it, causing the connection to sever and the machine to explode. With the gravitational disruption gone, Hardy flies the transport closer to Zod's ship but it is intercepted by Faora, who attempts to stop them.
As well, Zod has arrived in Metropolis with the ship. As he attempts to destroy the Air Force plane, Clark swoops in and crashes into the ship's control panel. Zod yells for Clark to once again let him complete his plan to revive Krypton. "Krypton had its chance," yells Clark, who then uses his heat-vision to tear apart the ship, causing it to crash and the gestation chamber to fracture.
Faora's attempts fail as well as Hardy steers the plane into the ship. As Lois was on the rear of the plane as it tilted down towards the ship, she loses her balance and falls to Earth. The collision of the two Phantom Drives causes the military aircraft and the Black Zero (along with the people on the vessels) to disappear.
Clark manages to save Lois again and puts her safely on the ground. Nearby, the sound of moving metal is heard, and Clark finds Zod, thoroughly enraged. Zod tells Clark that he was engineered to be a General of Krypton and to protect it and its people. With nothing left to revive the planet, Zod seethes that Clark has taken his soul and promises to kill the humans one at a time in retribution for what Clark has done.
The two then battle across Metropolis, smashing through buildings. During the fight, Zod adapts further to Earth's atmosphere, spawning heat-vision and the ability for flight. The battle soon ends with them in a train station, where Zod blasts his heat vision at a nearby family. "If you love these people so much, then you can mourn for them," he shouts. Clark begs Zod to stop but when Zod claims he will never stop, Clark snaps the General's neck, killing him. It is clear that Clark did not want to exact such a terrible judgement, and he agonizes over having not only killed another person, but one of the last of his race. Lois appears and comforts him.
Some time later, Swanwick and (Christina Wren) find Superman downing an Air Force drone. Superman claims that he knows they had sent it to find his home on Earth but he wants the search to stop. He vows that he will continue to fight for what is right and the security of Earth. The General questions Superman's commitment to which Clark replies that he's from Kansas and can be trusted. As he flies away, the General's adjutant smiles, clearly won over by how handsome and forthright he appears to be.
Clark then returns to Smallville, where he and Martha visit Jonathan's grave. Clark claims he wishes his father could have seen what he accomplished, but says he did. When she asks what Clark intends to do now, he claims he'll get a job where he can be updated on what is going on with the world, where he won't be questioned about visiting dangerous places, and where he will be able to ask questions if needed.
We then see him in the Daily Planet building, being introduced to Lois Lane. Though he is now sporting a pair of black-rimmed glasses, it is apparent that Lois knows just who this new employee is.